Mapping the 3D Genome Landscape

 描述：基因组的三维结构组织在核功能中起着关键作用，如基因表达和DNA复制。生物学的下一个重大挑战之一是确定详细的3D基因组结构并阐明其功能含义。在这个提案中，我们的目标是开发一套新的基因组结构和动态分析技术，从两个方面进行：(1)基因组DNA的空间相互作用和高阶组织；(2)驱动基因组三维折叠的蛋白质复合体的功能组织。本文提出的新的计算和实验方法集成了多个实验输入，并生成了3D核基因组组织的物理高阶模型。对这些模型的分析将对基因组在空间和时间上的三维组织的原理和结构/功能关系产生新的见解。我们有以下目标：(1)开发绘制基因组DNA在核中的相对空间位置的技术：我们的重点将是所有当前绘制技术所面临的三大技术障碍，即低效和潜在的偏见数据获取，缺乏时间分辨率，以及丢失更高顺序的联系信息。(2)开发破译3D基因组组织的“蛋白质密码”的技术：我们将采用一种成熟的管道来分离天然蛋白质复合体，但为了读出每个特定染色质相互作用区周围的染色质相互作用体，我们将进行广泛的优化。(3)开发三维基因组结构建模与分析技术：我们将开发基于群体的三维基因组结构建模的集成平台，并开发一系列计算工具来进行三维基因组的结构-功能图谱。(4)开发已售出的验证技术，以指导上述技术创新：我们将开发一套易于实施和易于解释的技术来验证我们的新技术，该技术可被社区普遍采用，用于类似的验证目的。

 DESCRIPTION: The 3D structural organization of the genome plays a key role in nuclear functions such as gene expression and DNA replication. One of the next grand challenges of biology is to determine the detailed 3D genome architecture and elucidate its functional implications. In this proposal, we aim to develop a suite of novel technologies for comprehensive structural and dynamic analyses of genomes, in two aspects: (1) the spatial interactions and higher-order organization of genomic DNA and (2) the functional organization of protein complexes driving the 3D folding of genomes. The new computational and experimental methods proposed herein integrate multiple experimental inputs and generate physical higher-order models of the 3D nuclear genome organization. Analysis of these models will yield new insights into the principles and structure/functions relationships of the genome's 3D organization in space and time. We have the following aims: (1) Develop technologies for mapping the relative spatial positions of genomic DNA in the nucleus: our focus will be on the three major technical barriers faced by all current mapping technologies, namely inefficient and potentially biased data acquisition, lack of temporal resolution, and missing higher-order contact information. (2) Develop technologies for deciphering the "Protein Code" of 3D genome organizations: we will employ a proven pipeline for the isolation of native protein complexes, but extensively optimized for the purpose of reading out the chromatin interactome surrounding each particular chromatin interacting region. (3) Develop technologies for modeling and analysis of 3D genome structures: we will develop an integrated platform for population-based modeling of 3D genome structures, and develop a series of computational tools to perform structure-function mapping on the 3D genomes. (4) Develop sold validation techniques for guiding the above technology innovations: we will develop a set of simple-to-implement and easy-to-interpret techniques to validate our novel technologies, and this techniques can be generally adopted by the community for similar validation purposes.